Questions tagged [molecular-interactions]

Questions related to molecular interactions when calculating quantities in materials science.

Filter by
Sorted by
Tagged with
20 votes
2 answers
1k views

Does increasing Lennard-Jones cutoff means higher accuracy?

I am currently trying to simulate a large box of QM/MM water molecules with SPC/Fw model and GGA DFT functional (a cube of 40 angstrom sides). To validate the QM and MM simulations separately, I am ...
mykd's user avatar
  • 2,282
17 votes
1 answer
268 views

Fermi level change in surfaces with adsorbed molecules

In a DFT standard calculation of a solid 3D material (i.e. bulk metal), one of the properties that can be obtained is the Fermi level $E_F$. This feature is related with the required work to add an ...
SalvaCardona's user avatar
  • 1,590
16 votes
1 answer
98 views

Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
Buck Thorn's user avatar
15 votes
1 answer
5k views

How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
SaiSmaran S B PES1201701189PES's user avatar
13 votes
1 answer
174 views

What are the steps to prepare a surface for molecular adsorption simulations on it?

I want to study the interaction of a given surface with some molecules. How should I prepare the surface for that kind of simulation? By prepare the surface I mean how many atom layers, how many of ...
Camps's user avatar
  • 22.9k
12 votes
1 answer
2k views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
SaiSmaran S B PES1201701189PES's user avatar
12 votes
1 answer
239 views

Rule-of-thumb for Morse potential cutoff in molecular dynamics?

Is there a rule-of-thumb for selecting a cutoff for the Morse potential in molecular dynamics simulation? For instance, is it typically some multiple of the equilibrium distance?
anneb101's user avatar
  • 985
11 votes
1 answer
678 views

Get fractional coordinates from special Wyckoff positions

I'm trying to get the fractional coordinates for $\ce{Mo}$ and $\ce{MoS_2-2H}$ in $\ce{MoS_2-2H}$, where 2H is the phase. $\ce{MoS_2-2H}$ is a bilayer, in which each layer is separated from each other ...
Carmen González's user avatar
8 votes
2 answers
148 views

Can the NCI (noncovalent interaction) index be generated starting with psi4?

Can NCI[1] index plots be generated starting from psi4? I'd be happy to just generate the NCI index values and mesh the isosurface myself. With a long-term goal to visualise various medicinal-...
lewiso1's user avatar
  • 936
8 votes
2 answers
409 views

Silica (α-cristobalite) water system generation

I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
WhiteLeo9's user avatar
  • 183
8 votes
2 answers
122 views

References for Electrostatics Calculations Used in Molecular Dynamics

I'm looking for classic references that describe the usual electrostatic contributions which have to be calculated in molecular dynamics simulations. I find it very hard to apprehend what different ...
jheindel's user avatar
  • 3,534
8 votes
0 answers
53 views

The effect of different mediums on the molecular orbital energies [closed]

I want to study the effect of different mediums, gas and various solvents, on the energy of the 10th highest molecular orbital of multiple quinones, which I obtained by a Gaussian software calculation....
sarra6's user avatar
  • 579
7 votes
2 answers
187 views

Which equation makes it possible to calculate the forces of attraction between a surface and molecules?

Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation? [Clarification 1] Between a ...
SFriendly's user avatar
  • 877
7 votes
1 answer
508 views

How to calculate the energy of a surface?

I want to study the interaction of a surface with some molecules (green house effect gases). To obtain the binding energy, the procedure is to calculate the energy of both systems separately $E_\...
Camps's user avatar
  • 22.9k
7 votes
0 answers
270 views

What does the shape of the radial distribution function(RDF) indicate? [closed]

From my understanding, generally in the RDF plot for liquids, the value of $g(r)$ goes to a maximum near the first solvation shell and then goes to a minimum and then slowly tapers off to the value of ...
Kavya Mrudula's user avatar
7 votes
0 answers
153 views

How to analyse structure factors calculated from a mixture of isotropic amorphous substrates

I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
mykd's user avatar
  • 2,282
7 votes
0 answers
90 views

Is there a software package to analyse interactions in crystals? [closed]

I have been using Quantum ESPRESSO, specifically the pp.x module to study interactions via charge density plots. The process is slow as for crystals containing ...
Hydrogen's user avatar
  • 159
6 votes
1 answer
154 views

Do we have specific benchmarks for the speed of a simulation of an empty water box with different water models?

I'm looking for a simulation of different water models (TIP3P, SPC/E, TIP4P, water models with flexible bounds) where the differences in simulation speeds on a common architecture are really seen. ...
sycramore's user avatar
  • 273
6 votes
1 answer
133 views

Can radial distribution function determine where the interactions of reference (atom/molecule) reduces greatly with surrounding atoms/molecules?

By plotting the RDF (radial distribution function), is it possible to determine at what radius the interactions of surrounding atoms/molecules with the reference atom/molecule reduce greatly? My ...
Night Shade's user avatar
5 votes
1 answer
66 views

What are the more efficient, or easier, methods of handling electromagnetic interactions?

Since metals, metalloids, non-metals, and composites, have differing characteristics, plug-and-play methods, so to speak, would be useful. Also, as it’s well known that a moving electrical field ...
M. Y. Zuo's user avatar
  • 153
4 votes
1 answer
52 views

What is the significance of xtb message: Interaction energies are not physical?

I have been exploring xtb and used it to run docking on an ion pair. I get the message at the end in the .log file. The xyz files of input structures were obtained from Gaussian output files. Is there ...
bhopshang's user avatar
  • 233
4 votes
1 answer
241 views

VASP with VDW dispersion corrections for a large system

I have been trying to find the binding energy of a water molecule with a crystalline silica slab and want to use vasp. whenever I try to use vasp for this purpose i get this error. Also, can someone ...
Xdrake's user avatar
  • 531
4 votes
2 answers
120 views

Non-Covalent Interaction between drug and DNA?

I am using classical molecular dynamics (MD) to observe a non-covalent interaction between my complex and the DNA, but there is a problem in that the complex interacts with the terminal of the DNA for ...
Abd-Elazeem Mohamed's user avatar
4 votes
0 answers
45 views

MMGBSA: Electrostatic and van der Waals

I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model ...
Bruce Zhou's user avatar
3 votes
2 answers
114 views

Adsorption of naphthalene on graphene oxide sheets with gmx

How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?
Mohamed El-amine's user avatar
3 votes
1 answer
121 views

PSI4 SAPT calculation: failure to write

I am attempting to run SAPT0 calculations on dimer complexes with around 100 atoms each. However, PSI4 SAPT0 calculations freeze and get terminated with the following error messages - I assigned 48GB ...
bhopshang's user avatar
  • 233
2 votes
1 answer
229 views

How to calculate ionic radius in Gaussian?

I am working with lithium sulfate and am wondering how to figure out the ionic radius of the Li atoms. I did a DFT/B3LYP/G-311G ++ (d,p) calculation.
Shelby Franke's user avatar
2 votes
0 answers
30 views

Interaction energy of two cartesian quadrupoles?

I am looking for a complete description of the interaction of two traceless cartesian quadrupoles. Even just an implementation online would be quite useful. The problem I am having is many of the ...
jheindel's user avatar
  • 3,534
2 votes
0 answers
20 views

Simple models for the energetic stabilization associated with damped polarizabilities of anions in solution [closed]

For many molecules, the gas-phase molecular polarizability, $\alpha_{gas}$ is approximately the same as that in the liquid, $\alpha_{liq.}$. For instance, $\ce{H2O}$, has roughly the same average $\...
jheindel's user avatar
  • 3,534
2 votes
0 answers
53 views

How to calculate the forces of attraction between a surface and molecules of a substance at a corrosion affection? [closed]

Previously, a question was asked about an equation that is able to calculate the forces of attraction between a surface and molecules (of another substance). During the discussion of the question a ...
SFriendly's user avatar
  • 877